Variant report

Variant	rs399299
Chromosome Location	chr5:179286097-179286098
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr5:179285476-179286136	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr5:179285151-179286397	K562	blood:	n/a	chr5:179285705-179285715
3	HNF4A	chr5:179285891-179286389	HepG2	liver:	n/a	chr5:179286227-179286240 chr5:179286225-179286243 chr5:179286226-179286241 chr5:179286228-179286240 chr5:179286227-179286241
4	SIN3AK20	chr5:179285536-179286266	HepG2	liver:	n/a	n/a
5	MAZ	chr5:179285159-179286154	Hela-S3	cervix:	n/a	chr5:179285705-179285715
6	ZMIZ1	chr5:179285164-179286325	K562	blood:	n/a	n/a
7	TCF7L2	chr5:179285798-179286428	PANC-1	pancreas:	n/a	chr5:179286231-179286238
8	ZBTB7A	chr5:179285205-179286494	K562	blood:	n/a	n/a
9	POLR2A	chr5:179285536-179286450	A549	lung:	n/a	n/a
10	PML	chr5:179285473-179286285	K562	blood:	n/a	n/a
11	POLR2A	chr5:179285462-179286532	ProgFib	skin:	n/a	n/a
12	MAX	chr5:179285364-179286338	NB4	blood:	n/a	chr5:179285705-179285715
13	TCF12	chr5:179285104-179286524	A549	lung:	n/a	chr5:179286343-179286353 chr5:179285348-179285355
14	ELF1	chr5:179285530-179286349	K562	blood:	n/a	chr5:179286306-179286318 chr5:179286305-179286314 chr5:179286239-179286251
15	SIN3AK20	chr5:179285509-179286107	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr5:179285549-179286445	HUVEC	blood vessel:	n/a	n/a
17	SP2	chr5:179285796-179286127	K562	blood:	n/a	chr5:179285939-179285954
18	HDAC2	chr5:179285626-179286362	HepG2	liver:	n/a	n/a
19	CTCF	chr5:179286000-179286150	A549	lung:	n/a	n/a
20	CHD2	chr5:179285603-179286256	HepG2	liver:	n/a	n/a
21	SMC3	chr5:179285739-179286436	K562	blood:	n/a	n/a
22	POLR2A	chr5:179285421-179286473	GM12892	blood:	n/a	n/a
23	HCFC1	chr5:179285613-179286424	K562	blood:	n/a	n/a
24	ELK1	chr5:179286055-179286173	K562	blood:	n/a	n/a
25	CTCF	chr5:179286000-179286150	HAc	cerebellar:	n/a	n/a
26	ZBTB33	chr5:179285659-179286153	HCT-116	colon:	n/a	n/a
27	POLR2A	chr5:179285405-179286342	Hela-S3	cervix:	n/a	n/a
28	TAF1	chr5:179285510-179286426	HepG2	liver:	n/a	n/a
29	MYC	chr5:179285642-179286377	K562	blood:	n/a	chr5:179285705-179285715
30	HEY1	chr5:179285619-179286288	HepG2	liver:	n/a	chr5:179285847-179285862 chr5:179285850-179285865
31	EGR1	chr5:179285154-179286684	HCT-116	colon:	n/a	chr5:179285574-179285583 chr5:179286279-179286293 chr5:179285571-179285584 chr5:179285866-179285875 chr5:179285571-179285584 chr5:179286281-179286291 chr5:179286241-179286251 chr5:179286280-179286293 chr5:179286277-179286291 chr5:179286303-179286316 chr5:179286281-179286291 chr5:179285567-179285589 chr5:179285571-179285584 chr5:179285705-179285718 chr5:179286388-179286401 chr5:179286281-179286292 chr5:179285865-179285874 chr5:179286295-179286309 chr5:179286388-179286401 chr5:179286281-179286292 chr5:179286281-179286290 chr5:179285574-179285584
32	CREB1	chr5:179285512-179286445	A549	lung:	n/a	n/a
33	POLR2A	chr5:179285580-179286588	HL-60	blood:	n/a	n/a
34	POLR2A	chr5:179285319-179286369	GM15510	blood:	n/a	n/a
35	EP300	chr5:179285699-179286235	HepG2	liver:	n/a	n/a
36	TAF1	chr5:179285187-179286277	H1-neurons	neurons:	n/a	n/a
37	TAF1	chr5:179285666-179286172	PFSK-1	brain:	n/a	n/a
38	YY1	chr5:179285043-179286150	GM12878	blood:	n/a	chr5:179285366-179285375 chr5:179285849-179285858 chr5:179285849-179285860
39	RCOR1	chr5:179285239-179286388	K562	blood:	n/a	n/a
40	CTCF	chr5:179285980-179286130	HCFaa	heart:	n/a	n/a
41	TCF12	chr5:179285429-179286375	ECC-1	luminal epithelium:	n/a	chr5:179286343-179286353
42	MYBL2	chr5:179285272-179286308	HepG2	liver:	n/a	n/a
43	YY1	chr5:179285514-179286156	GM12878	blood:	n/a	chr5:179285849-179285858 chr5:179285849-179285860
44	EP300	chr5:179285634-179286213	GM12878	blood:	n/a	n/a
45	TBL1XR1	chr5:179285645-179286198	K562	blood:	n/a	n/a
46	RAD21	chr5:179285746-179286098	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr5:179285638-179286205	K562	blood:	n/a	n/a
48	RAD21	chr5:179285801-179286126	HepG2	liver:	n/a	n/a
49	POLR2A	chr5:179285177-179286489	K562	blood:	n/a	n/a
50	TCF12	chr5:179285164-179286543	ECC-1	luminal epithelium:	n/a	chr5:179286343-179286353 chr5:179285348-179285355

No.	Distal block	Cell Line	Cell type
1	chr5:179246365..179250489-chr5:179281961..179288216,8	MCF-7	breast:
2	chr5:179262940..179266304-chr5:179284329..179288957,4	K562	blood:
3	chr5:179124684..179126939-chr5:179285490..179289046,3	MCF-7	breast:
4	chr5:179227703..179229883-chr5:179285735..179288229,2	K562	blood:
5	chr5:179246544..179252042-chr5:179284250..179287282,6	K562	blood:
6	chr5:179245762..179250347-chr5:179281858..179288397,17	MCF-7	breast:
7	chr5:179285948..179288985-chr5:179497401..179500729,4	K562	blood:
8	chr5:179284415..179287305-chr5:179333085..179336223,5	MCF-7	breast:
9	chr5:179284745..179287378-chr5:179287865..179289416,2	K562	blood:
10	chr5:179285802..179287373-chr5:179498927..179500668,2	MCF-7	breast:
11	chr5:179232749..179234437-chr5:179284019..179286391,2	K562	blood:
12	chr5:179285279..179287519-chr5:179287534..179289534,3	MCF-7	breast:
13	chr5:179244299..179249031-chr5:179283718..179288072,6	K562	blood:
14	chr5:179227703..179229883-chr5:179285735..179289127,3	K562	blood:
15	chr5:179221198..179223904-chr5:179283563..179286738,3	MCF-7	breast:
16	chr5:179285987..179287986-chr5:179498943..179500555,2	K562	blood:
17	chr5:179221892..179226661-chr5:179285311..179287197,6	MCF-7	breast:
18	chr5:179249726..179253531-chr5:179284409..179289652,9	K562	blood:
19	chr5:179285301..179288103-chr5:179290972..179294711,5	MCF-7	breast:
20	chr5:179229039..179235504-chr5:179284286..179287391,9	MCF-7	breast:
21	chr5:179284572..179287253-chr5:179332885..179335031,4	MCF-7	breast:
22	chr5:179284411..179288482-chr5:179291303..179294641,8	MCF-7	breast:
23	chr5:179263394..179265820-chr5:179284622..179286791,2	MCF-7	breast:

Variant related genes	Relation type
C5orf45	TF binding region
ENSG00000113269	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000221394	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10075090	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs441659	0.87[AMR][1000 genomes]
rs61736195	1.00[EUR][1000 genomes]
rs6861674	1.00[EUR][1000 genomes]
rs72813735	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
9	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179284400-179286600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr5:179284600-179286400	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr5:179284600-179286600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:179284600-179286600	Active TSS	Brain Angular Gyrus	brain
5	chr5:179284600-179286600	Active TSS	Duodenum Mucosa	Duodenum
6	chr5:179284600-179286600	Active TSS	Fetal Intestine Large	intestine
7	chr5:179284600-179286600	Active TSS	Ovary	ovary
8	chr5:179284600-179286600	Active TSS	HSMMtube	muscle
9	chr5:179284600-179286600	Active TSS	K562	blood
10	chr5:179284600-179286600	Active TSS	Osteobl	bone
11	chr5:179284600-179286800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:179284600-179286800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:179284600-179286800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:179284600-179286800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:179284600-179286800	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr5:179284600-179286800	Active TSS	Rectal Smooth Muscle	rectum
17	chr5:179284600-179287000	Active TSS	A549	lung
18	chr5:179284600-179287000	Active TSS	HSMM	muscle
19	chr5:179284600-179287200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr5:179284600-179287200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr5:179284800-179286200	Active TSS	Stomach Smooth Muscle	stomach
22	chr5:179284800-179286400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr5:179284800-179286400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr5:179284800-179286400	Active TSS	GM12878-XiMat	blood
25	chr5:179284800-179286600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:179284800-179286600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:179284800-179286600	Active TSS	Brain Hippocampus Middle	brain
28	chr5:179284800-179286600	Active TSS	Brain Substantia Nigra	brain
29	chr5:179284800-179286800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179284800-179286800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr5:179284800-179286800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:179284800-179286800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:179284800-179286800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr5:179284800-179286800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:179284800-179286800	Active TSS	Brain Anterior Caudate	brain
36	chr5:179284800-179286800	Active TSS	Colon Smooth Muscle	Colon
37	chr5:179284800-179286800	Active TSS	Fetal Brain Female	brain
38	chr5:179284800-179286800	Active TSS	Fetal Intestine Small	intestine
39	chr5:179284800-179287000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:179284800-179287000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:179284800-179287000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:179284800-179287000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr5:179284800-179287000	Active TSS	NHLF	lung
44	chr5:179284800-179287200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr5:179285000-179286200	Active TSS	Pancreas	Pancrea
46	chr5:179285000-179286200	Active TSS	Stomach Mucosa	stomach
47	chr5:179285000-179286200	Active TSS	Thymus	Thymus
48	chr5:179285000-179286200	Active TSS	Spleen	Spleen
49	chr5:179285000-179286200	Bivalent/Poised TSS	HepG2	liver
50	chr5:179285000-179286400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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